I had a silimilar problem and it was caused by a lower BT version on the car. I suspect the note 4 has the very latest version 4 and toyota haven't caught up.

You could try a different music manager or see whether there is an app to make it backwards compatible.

 

I think it's probably the BT codec that the Note 4 is using also.

Try PowerAmp or some other music player besides stock and see if that helps. Otherwise you will have to wait for Toyota to update their firmware.

 

I've got a 2013 Prius and the Note 4 plays music fine with mine.

Try going in to the phone and/or bluetooth settings on the Prius and make sure that 'connected for music' is selected.
If that doesn't work try removing the pairing on the Prius and then re-pair them. The display on the Prius should say something like 'connected for phone and music' - make sure the 'and music' is there.

If all else fails try taking it to the local Toyota dealer to see if there is some sort of an upgrade available for the Prius itself (not the Entune app).

Good luck

 

What year is your Prius?

That kind of problem (music plays but controls do not respond) is the same problem I had with my Jeep's UConnect system a couple of years ago. Once Chrysler updated the firmware to the current BT standard, it worked just fine.

My Note 4 paired up with the Jeep without a problem, so I suspect the firmware on your radio is not up to date.